UMAP projections show sample groups (left), cell type annotations (middle), and CHIKV+ cells (right).
The fraction of cells passing QC filtering cutoffs is shown for each sample.
The fraction of CHIKV+ cells passing QC filtering cutoffs is shown for each sample.
UMAP projections show macrophage subsets
Module scores for Culemann et al. gene lists are shown for each macrophage cluster. Clusters are colored based on the assigned subset labels.
Heatmaps show mean expression of Culemann et al. gene lists. Replicates are shown separately for each macrophage subset.
UMAP projections show CHIKV+ cells (left) and CHIKV-high clusters (middle, right) for CHIKV-infected samples.
The fraction of cells that are CHIKV+ is shown for each replicate from each macrophage subset. P values were calculated by pooling replicates together, using a hypergeometric test with Bonferroni correction.
Top upregulated genes associated with inflammatory disease are shown below for mock- vs CHIKV-infected macrophages.
Top genes upregulated in CHIKV-infected mice are shown below for each macrophage subset.
Genes upregulated in T cells from CHIKV vs mock-infected mice are shown below. All CD4+ or CD8+ T cells were grouped together.
Ifng expression is shown below for each T cell subset